We present a simple route to prepare hierarchical structures by allowing the partial diffusion of polymer microspheres into the nanopores of anodic aluminum oxide (AAO) templates. Polystyrene (PS) microspheres were first spread onto a silicon substrate and allowed to self-assemble into well-ordered monolayers of the microspheres. Upon heating above the glass-transition temperature, diffusion of the PS into the pores of the AAO occurred only at pores of the microspheres in contact with the membrane. After the removal of the AAO membrane, ordered arrays of microspheres capped with nanorods were produced, yielding surfaces with topographies spanning multiple length scales. Control over the nanoscopic and microscopic length scales can be trivially achieved by changing the size of the microspheres and the diameter of the pores in the membranes.